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Merge remote-tracking branch 'origin/release/0.4.0' into main
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‎.gitignore‎

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‎dsf-bpe-process-feasibility/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<artifactId>dsf-bpe-process-feasibility</artifactId>
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<parent>
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<artifactId>dsf-bpe-highmed-processes-pom</artifactId>
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<groupId>org.highmed.dsf</groupId>
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<version>0.4.0</version>
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</parent>
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<dependencies>
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<dependency>
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<groupId>org.highmed.dsf</groupId>
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<artifactId>dsf-bpe-process-base</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-annotations</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>de.hs-heilbronn.mi</groupId>
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<artifactId>log4j2-utils</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.highmed.dsf</groupId>
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<artifactId>dsf-fhir-validation</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.highmed.dsf</groupId>
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<artifactId>dsf-bpe-process-base</artifactId>
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<scope>test</scope>
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<type>test-jar</type>
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</dependency>
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</dependencies>
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<profiles>
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<profile>
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<id>copy-to-highmed-dsf-process</id>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-dependency-plugin</artifactId>
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<executions>
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<execution>
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<id>copy-process-plugin-to-docker-test-setup</id>
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<phase>package</phase>
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<goals>
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<goal>copy</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</artifactItem>
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</artifactItems>
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<outputDirectory>../../highmed-dsf/dsf-docker-test-setup/bpe/app/process</outputDirectory>
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</configuration>
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</execution>
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<execution>
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<id>copy-process-plugin-to-docker-test-setup-3medic-ttp/medic1</id>
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<phase>package</phase>
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<goals>
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<goal>copy</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</artifactItem>
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</artifactItems>
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<outputDirectory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic1/bpe/app/process</outputDirectory>
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</configuration>
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</execution>
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<execution>
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<id>copy-process-plugin-to-docker-test-setup-3medic-ttp/medic2</id>
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<phase>package</phase>
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<goals>
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<goal>copy</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</artifactItem>
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</artifactItems>
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<outputDirectory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic2/bpe/app/process</outputDirectory>
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</configuration>
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</execution>
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<execution>
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<id>copy-process-plugin-to-docker-test-setup-3medic-ttp/medic3</id>
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<phase>package</phase>
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<goals>
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<goal>copy</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</artifactItem>
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</artifactItems>
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<outputDirectory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic3/bpe/app/process</outputDirectory>
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</configuration>
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</execution>
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<execution>
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<id>copy-process-plugin-to-docker-test-setup-3medic-ttp/ttp</id>
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<phase>package</phase>
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<goals>
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<goal>copy</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</artifactItem>
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</artifactItems>
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<outputDirectory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/ttp/bpe/app/process</outputDirectory>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-clean-plugin</artifactId>
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<configuration>
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<filesets>
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<fileset>
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<directory>../../highmed-dsf/dsf-docker-test-setup/bpe/app/process</directory>
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<includes>
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<include>${project.artifactId}-${project.version}.jar</include>
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</includes>
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<followSymlinks>false</followSymlinks>
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</fileset>
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<fileset>
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<directory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic1/bpe/app/process</directory>
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<includes>
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<include>${project.artifactId}-${project.version}.jar</include>
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</includes>
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<followSymlinks>false</followSymlinks>
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</fileset>
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<fileset>
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<directory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic2/bpe/app/process</directory>
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<includes>
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<include>${project.artifactId}-${project.version}.jar</include>
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</includes>
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<followSymlinks>false</followSymlinks>
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</fileset>
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<fileset>
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<directory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/medic3/bpe/app/process</directory>
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<includes>
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<include>${project.artifactId}-${project.version}.jar</include>
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</includes>
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<followSymlinks>false</followSymlinks>
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</fileset>
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<fileset>
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<directory>../../highmed-dsf/dsf-docker-test-setup-3medic-ttp/ttp/bpe/app/process</directory>
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<includes>
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<include>${project.artifactId}-${project.version}.jar</include>
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</includes>
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<followSymlinks>false</followSymlinks>
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</fileset>
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</filesets>
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</configuration>
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</plugin>
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</plugins>
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</build>
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</profile>
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</profiles>
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</project>

‎dsf-bpe-process-feasibility/src/main/java/org/highmed/dsf/bpe/ConstantsFeasibility.java‎

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package org.highmed.dsf.bpe;
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import static org.highmed.dsf.bpe.ConstantsBase.PROCESS_HIGHMED_URI_BASE;
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import static org.highmed.dsf.bpe.FeasibilityProcessPluginDefinition.VERSION;
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public interface ConstantsFeasibility
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{
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String BPMN_EXECUTION_VARIABLE_RESEARCH_STUDY = "researchStudy";
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String BPMN_EXECUTION_VARIABLE_NEEDS_CONSENT_CHECK = "needsConsentCheck";
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String BPMN_EXECUTION_VARIABLE_NEEDS_RECORD_LINKAGE = "needsRecordLinkage";
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String BPMN_EXECUTION_VARIABLE_BLOOM_FILTER_CONFIG = "bloomFilterConfig";
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String BPMN_EXECUTION_VARIABLE_COHORTS = "cohorts";
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String BPMN_EXECUTION_VARIABLE_QUERIES = "queries";
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String BPMN_EXECUTION_VARIABLE_QUERY_RESULTS = "queryResults";
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String BPMN_EXECUTION_VARIABLE_FINAL_QUERY_RESULTS = "finalQueryResults";
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String BPMN_EXECUTION_ERROR_CODE_MULTI_MEDIC_RESULT = "errorMultiMedicFeasibilityResult";
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// Must be 3 or larger, as otherwise it is possible to draw conclusions about the individual MeDICs
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// (if I already know the cohort size in my MeDIC)
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int MIN_PARTICIPATING_MEDICS = 3;
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int MIN_COHORT_DEFINITIONS = 1;
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String FEASIBILITY_QUERY_PREFIX = "select count";
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String CODESYSTEM_HIGHMED_FEASIBILITY = "http://highmed.org/fhir/CodeSystem/feasibility";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_PARTICIPATING_MEDIC_CORRELATION_KEY = "medic-correlation-key";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_NEEDS_CONSENT_CHECK = "needs-consent-check";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_NEEDS_RECORD_LINKAGE = "needs-record-linkage";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_BLOOM_FILTER_CONFIG = "bloom-filter-configuration";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_SINGLE_MEDIC_RESULT = "single-medic-result";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_SINGLE_MEDIC_RESULT_REFERENCE = "single-medic-result-reference";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_PARTICIPATING_MEDICS_COUNT = "participating-medics";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_NOT_ENOUGH_PARTICIPATION = "not-enough-participation";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_MULTI_MEDIC_RESULT = "multi-medic-result";
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String CODESYSTEM_HIGHMED_FEASIBILITY_VALUE_RESEARCH_STUDY_REFERENCE = "research-study-reference";
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String PROFILE_HIGHMED_TASK_REQUEST_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-request-feasibility";
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String PROFILE_HIGHMED_TASK_REQUEST_FEASIBILITY_PROCESS_URI = PROCESS_HIGHMED_URI_BASE + "requestFeasibility/";
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String PROFILE_HIGHMED_TASK_REQUEST_FEASIBILITY_PROCESS_URI_AND_LATEST_VERSION =
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PROFILE_HIGHMED_TASK_REQUEST_FEASIBILITY_PROCESS_URI + VERSION;
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String PROFILE_HIGHMED_TASK_REQUEST_FEASIBILITY_MESSAGE_NAME = "requestFeasibilityMessage";
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String PROFILE_HIGHMED_TASK_LOCAL_SERVICES_PROCESS_URI = PROCESS_HIGHMED_URI_BASE + "localServicesIntegration/";
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String PROFILE_HIGHMED_TASK_EXECUTE_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-execute-feasibility";
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String PROFILE_HIGHMED_TASK_EXECUTE_FEASIBILITY_PROCESS_URI = PROCESS_HIGHMED_URI_BASE + "executeFeasibility/";
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String PROFILE_HIGHMED_TASK_EXECUTE_FEASIBILITY_PROCESS_URI_AND_LATEST_VERSION =
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PROFILE_HIGHMED_TASK_EXECUTE_FEASIBILITY_PROCESS_URI + VERSION;
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String PROFILE_HIGHMED_TASK_EXECUTE_FEASIBILITY_MESSAGE_NAME = "executeFeasibilityMessage";
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String PROFILE_HIGHMED_TASK_COMPUTE_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-compute-feasibility";
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String PROFILE_HIGHMED_TASK_COMPUTE_FEASIBILITY_PROCESS_URI = PROCESS_HIGHMED_URI_BASE + "computeFeasibility/";
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String PROFILE_HIGHMED_TASK_COMPUTE_FEASIBILITY_PROCESS_URI_AND_LATEST_VERSION =
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PROFILE_HIGHMED_TASK_COMPUTE_FEASIBILITY_PROCESS_URI + VERSION;
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String PROFILE_HIGHMED_TASK_COMPUTE_FEASIBILITY_MESSAGE_NAME = "computeFeasibilityMessage";
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String PROFILE_HIGHMED_TASK_SINGLE_MEDIC_RESULT_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-single-medic-result-feasibility";
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String PROFILE_HIGHMED_TASK_SINGLE_MEDIC_RESULT_FEASIBILITY_MESSAGE_NAME = "resultSingleMedicFeasibilityMessage";
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String PROFILE_HIGHMED_TASK_MULTI_MEDIC_RESULT_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-multi-medic-result-feasibility";
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String PROFILE_HIGHMED_TASK_MULTI_MEDIC_RESULT_FEASIBILITY_MESSAGE_NAME = "resultMultiMedicFeasibilityMessage";
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String PROFILE_HIGHMED_TASK_ERROR_FEASIBILITY = "http://highmed.org/fhir/StructureDefinition/task-multi-medic-error-feasibility";
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String PROFILE_HIGHMED_TASK_ERROR_FEASIBILITY_MESSAGE_NAME = "errorMultiMedicFeasibilityMessage";
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}

‎dsf-bpe-process-feasibility/src/main/java/org/highmed/dsf/bpe/FeasibilityProcessPluginDefinition.java‎

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package org.highmed.dsf.bpe;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import java.util.stream.Stream;
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import org.highmed.dsf.bpe.spring.config.FeasibilityConfig;
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import org.highmed.dsf.bpe.spring.config.FeasibilitySerializerConfig;
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import org.highmed.dsf.fhir.resources.AbstractResource;
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import org.highmed.dsf.fhir.resources.ActivityDefinitionResource;
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import org.highmed.dsf.fhir.resources.CodeSystemResource;
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import org.highmed.dsf.fhir.resources.ResourceProvider;
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import org.highmed.dsf.fhir.resources.StructureDefinitionResource;
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import org.highmed.dsf.fhir.resources.ValueSetResource;
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import ca.uhn.fhir.context.FhirContext;
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public class FeasibilityProcessPluginDefinition implements ProcessPluginDefinition
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{
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public static final String VERSION = "0.4.0";
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@Override
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public String getName()
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{
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return "dsf-bpe-process-feasibility";
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}
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@Override
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public String getVersion()
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{
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return VERSION;
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}
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@Override
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public Stream<String> getBpmnFiles()
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{
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return Stream.of("bpe/requestFeasibility.bpmn", "bpe/computeFeasibility.bpmn", "bpe/executeFeasibility.bpmn");
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}
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@Override
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public Stream<Class<?>> getSpringConfigClasses()
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{
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return Stream.of(FeasibilityConfig.class, FeasibilitySerializerConfig.class);
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}
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@Override
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public ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader classLoader)
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{
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var aCom = ActivityDefinitionResource.file("fhir/ActivityDefinition/highmed-computeFeasibility.xml");
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var aExe = ActivityDefinitionResource.file("fhir/ActivityDefinition/highmed-executeFeasibility.xml");
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var aReq = ActivityDefinitionResource.file("fhir/ActivityDefinition/highmed-requestFeasibility.xml");
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var cF = CodeSystemResource.file("fhir/CodeSystem/highmed-feasibility.xml");
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var sTCom = StructureDefinitionResource.file("fhir/StructureDefinition/highmed-task-compute-feasibility.xml");
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var sTErr = StructureDefinitionResource.file("fhir/StructureDefinition/highmed-task-error-feasibility.xml");
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var sTExe = StructureDefinitionResource.file("fhir/StructureDefinition/highmed-task-execute-feasibility.xml");
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var sTResM = StructureDefinitionResource
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.file("fhir/StructureDefinition/highmed-task-multi-medic-result-feasibility.xml");
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var sTReq = StructureDefinitionResource.file("fhir/StructureDefinition/highmed-task-request-feasibility.xml");
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var sTResS = StructureDefinitionResource
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.file("fhir/StructureDefinition/highmed-task-single-medic-result-feasibility.xml");
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var vF = ValueSetResource.file("fhir/ValueSet/highmed-feasibility.xml");
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Map<String, List<AbstractResource>> resourcesByProcessKeyAndVersion = Map.of(
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"computeFeasibility/" + VERSION, Arrays.asList(aCom, cF, sTCom, sTResS, vF),
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"executeFeasibility/" + VERSION, Arrays.asList(aExe, cF, sTExe, vF),
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"requestFeasibility/" + VERSION, Arrays.asList(aReq, cF, sTReq, sTResM, sTErr, vF));
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return ResourceProvider
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.read(VERSION, () -> fhirContext.newXmlParser().setStripVersionsFromReferences(false), classLoader,
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resourcesByProcessKeyAndVersion);
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}
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}

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